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Time

Sunday, 11 Feb 2018 - Sunday, 18 Feb 2018

Topics

"Computational Biology, Computational Mathematics, Theoretical Biology, Bioinformatics, Biological Networks"

Registration Fee

280,- €

Available AV equipment

black board, overhead projector, beamer, laptop (linux) network, internet access via Wlan

Participants

Location(s)

Villa Plemelj
Prešernova 39
4260 Bled, Slovenia
Phone: +386 4 5743 023
GPS Coordinates: 46.371121,14.108504
Hotel Astoria
Prešernova 44
4260 Bled, Slovenia
Phone: +386 4 579 44 00
Fax:     +386 4 579 44 01


View Larger Map

How to get there
From Ljubljana airport you have the following options to get to the Winterseminar:
  • take a regular taxi (approx. 50 €)
  • public bus transfer, first to Ljubljana city and from there to Bled
  • Airport Shuttle ZUP prevozi (recommended, special rates for groups)
If you arrive via train at Lesce-Bled, you can take a taxi or go by bus to the main bus station (search for connections from Lesce to Bled)

Program

Arrival and Get Together at the Villa 11 Feb 20176pmVilla Plemlj
Opening Session 12 Feb 20174pmHotel Astoria
Session Chair: Ronny Lorenz
Slides Speaker Talk Title
Ronny LorenzWelcome and opening of the TBI Winterseminar
Manja MarzOpening Surprise Talk
Trudie StraussWord Frequency Distributions across Languages
Nancy RetzlaffCurrent projects in Digital Humanities
Berenice BatutBuilding an open, collaborative, online infrastructure for bioinformatics training
Anne WenzelNavigating the landscape of RNA bioinformatics tools by ontologies
Cheminformatics, Graphs, and Networks 12 Feb 20178pmHotel Astoria
Session Chair: Jakob Lykke Anderson
Slides Speaker Talk Title
Peter Severin RasmussenGraph Transformation, Atom Tracing, and Isotope Labelling
Waldeyr Mendes SilvaIn silico reconstruction of Copaifera multijuga Hayne terpenoids network
Patrick BraunMethods to randomize metabolic networks and classifiy them
Guillermo RestrepoNews on the history of chemistry through chemical reactions
Christoph FlammElectron-Bifurcation -- Life's 3rd mechanism of energy conservation
Viridae 13 Feb 20174pmHotel Astoria
Session Chair: Michael Wolfinger
Slides Speaker Talk Title
Kevin LamkiewiczSequencing with Raman-Spec(k)troscopy
Emanuel BarthHacken Progress Update
Clara MuellerTranscriptional regulation in Ebola Virus: The role of VP30
Roman OchsenreiterThe viral world as network of RNA structures
Daniel DesiroPrediction and evaluation of vRNA-vRNA interaction sites between influenza A wild type and mutant vRNPs
Sebastian KrautwurstRNA virus full genome sequencing and haplotype reconstruction
Florian MockChallenges of virus host prediction with Deep Learning
Transcriptomics 13 Feb 20178pmHotel Astoria
Session Chair: Stephan Bernhart
Slides Speaker Talk Title
Anela TosevskaAge-associated DNA methylation drift
Adrian GeisslerAnnotation and transcriptomic analysis of ncRNAs in bacterial enzyme production
Patricia SieberComparative study on alternative splicing in human-pathogenic fungi
Konstantin Riegede.STAIR Galaxy flavor for RNA-Seq analysis
Martin HoelzerPCAGO: An interactive web service to analyze RNA-Seq data with principal component analysis
Marie LataretuHow to find the mitochondrial genome in fungal assemblies.
Marcus LechnerRNA-Seq is more than differential gene expression: Ultra short transcripts and RNA processing
RNA I 14 Feb 20178pmHotel Astoria
Session Chair: Maria Waldl
Slides Speaker Talk Title
Maria Beatriz Walter CostaAlgorithms in ncRNA structure evolution
Stefan HammerA novel theophylline triggered RNAseP riboswitch
Sebastian WillVersatile fixed-parameter tractable sampling for multi-target RNA design
Stefan BadeltReaction enumeration and condensation of domain-level strand displacement systems
Jayashree KumarRNA structure and genetic variation in introns: the case for the riboSplitch
Joerg FallmannRNA-protein interactions on structure level
Group Photo 15 Feb 20183:30pmHotel Astoria (Entrance)
Graphs, Theory, Phylogenetics 15 Feb 20184pmHotel Astoria
Session Chair: Christian Hoener zu Siederdissen
Slides Speaker Talk Title
Tomaz PisanskiThe convexity defect of benzenoids
Nino BasicOn the Clar number of benzenoid graphs
Nikolas WiesekeThe path of trial and tribulation towards homology based species tree inference
Manuela GeissA characterization of colored Best Match Graphs
Yangjing LongPath relations and tree metrics
Fabian GaertnerThe Magic of Graph Databases
Bioinformatics 15 Feb 20178pmHotel Astoria
Session Chair: Joerg Fallmann
Slides Speaker Talk Title
Andre FujitaStatistics on biological networks
Dominik OttoMCMC of Dynamical Systems as Uncertainty Propagation of qPCR Data
Nadezhda DonchevaTissue-specific pathway comparison in mammalian organisms
Maximilian CollatzIn silico enrichment of immunodominant proteins
Oana PalascaIdentification of long non-coding RNAs in livestock species
Giulia CorsiEfficiency prediction for CRISPR Cas9
Florian HeylPredicting exon splicing changes triggered by methylation profiles
Algorithms, Graphs, and Networks 16 Feb 20174pmHotel Astoria
Session Chair: Marc Hellmuth
Slides Speaker Talk Title
Sarah Berkemer1 + Greedy + DP
Sven DziadekAutomata and Dynamic Programming
Lars Juhl JensenA crash course on STRING and Cytoscape
Mariam FarmanMSF- Modulated Sub-path Finder
Jakob Lykke AndersenCanonicalization of Data Structures
RNA II 16 Feb 20178pmHotel Astoria
Session Chair: Stefan Hammer
Slides Speaker Talk Title
Veerendra GadekarClustering RNA secondary structures in Arabidopsis thaliana
Jakob Hull HavgaardDotCodeR: Alignment of RNA secondary structure dotplots
Irene BeckmannIdentification and Classification of Peudoknots and their impact on RNA 3D structure prediction
Bernhard ThielLost in missing residues - Challenges while working with RNA structures from the Protein Data Base
Gregor EntzianImprove RNA secondary structure prediction with tertiary motifs
Afaf SaaidiModeling of RNA structures using an integrative Multi-Probing approach
Genomics 17 Feb 20174pmHotel Astoria
Session Chair: Marcus Lechner
Slides Speaker Talk Title
Halima SakerMultidimensional segmentation of Saccharomyces cerevisiae S288C
Sinem SuermeliEvolution of nmtRNAs in mammals
Jeremias ScheberaDetection of rearrangements in cancer genome with ChIP-seq data
Daniel WiegreffeIntroduction of the Supergenome Browser
Maria_WaldlPredicting RNA-RNA Interactions - A Kinetic Approach
Marcel WintersegemehlQC - a quality control tool for mapped NGS data
Micha SammethAutomated Functional Annotation of Protein Products of Alternatively Spliced Genes
Ronny LorenzConcluding Remarks
Discussion Groups 17 Feb 20178pmVilla Plemlj

Photos

Handover of the magic bottles
Handover of the magic bottles

Berenice Batut also took some very nice pictures of Bled and the surrounding area. You can find them at her Flickr page.
Take me there

Also Lars Juhl Jensen captured some nice impressions of lake Bled. You can find them at his 500px profile.
Take me there

Further Information

Find detailed information here.

Registered Participants

Name (headcount: 92) Email Affiliation
RonnyLorenzronny (at) tbi.univie.ac.atTBI Wien
StefanHammerstefan.hammer (at) uni-leipzig.deBioinformatik Uni Leipzig
PeterStadlerstadler (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
BärbelStadlerbaer (at) bioinf.uni-leipzig.deextern
Lars JuhlJensenlars.juhl.jensen (at) cpr.ku.dkCPR Copenhagen
JanGorodkingorodkin (at) rth.dkRTH Copenhagen
IvoHofackerivo (at) tbi.univie.ac.atTBI Wien
SebastianWillwill (at) tbi.univie.ac.atTBI Wien
JayashreeKumarjkumar12 (at) email.unc.eduUniversity of North Carolina, Chapel Hill
ManuelaGeissmanuela (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
NadezhdaDonchevadoncheva (at) rth.dkRTH Copenhagen
MarcelWintermarcel (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
JeremiasScheberaJeremias.schebera (at) gmail.comBioinformatik Uni Leipzig
DanielWiegreffedaniel (at) bioinf.uni-leipzig.deBSV Uni Leipzig
NicoleHinzmannhinzmann (at) informatik.uni-leipzig.deBSV Uni Leipzig
TaináRaioltaina.raiol (at) fiocruz.brFiocruz Brasília
AndressaValadaresandressarodrial (at) gmail.comUniversidade de Brasília
SinemSuermelisinemsrmeli (at) gmail.comBioinformatik Uni Leipzig
MichaelWolfingermichael.wolfinger (at) univie.ac.atTBI Wien
DanielMerkledaniel (at) imada.sdu.dkSDU Odense
Peter SeverinRasmussenperas13 (at) student.sdu.dkSDU Odense
EmanuelBarthemanuel.barth (at) uni-jena.deFSU Jena
KevinLamkiewiczkevin.lamkiewicz (at) uni-jena.deFSU Jena
DanielDesiròdaniel.desiro (at) uni-jena.deFSU Jena
MaximilianCollatzmaximilian.collatz (at) uni-jena.deFSU Jena
MariaWaldlmaria (at) tbi.univie.ac.atTBI Wien
MarieLataretumarie.lataretu (at) uni-jena.deFSU Jena
ChristophFlammxtof (at) tbi.univie.ac.atTBI Wien
Jakob LykkeAndersenjakob.lykke.andersen (at) univie.ac.atTBI Wien
MarcHellmuthmhellmuth (at) mailbox.orgUniv. Greifswald
PatriciaSieberpatricia.sieber (at) uni-jena.deFSU Jena
MartinHölzermartin.hoelzer (at) uni-jena.deFSU Jena
YangjingLonglongyangjing (at) gmail.comUni Greifswald
Halimasakerhalima (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
HermanStraussstrauss.trudie (at) gmail.comExternal
TrudieStraussstrauss.trudie (at) gmail.comUniversity of the Free State
Josenilto CarlosMendonca Juniorjoseniltojr (at) gmail.comBrazilian Post and Telegraph Company
FlorianMockflorian.mock (at) uni-jena.deFSU Jena
GuillermoRestreporestrepo (at) mis.mpg.deMPI MIS Leipzig
RojinKianianmcrojin (at) gmail.comSDU Odense
WilfriedImrichimrich (at) unileoben.ac.atUni Leoben
YannPontyyann.ponty (at) lix.polytechnique.frCNRS/Ecole Polytechnique
NinoBašićnino.basic (at) famnit.upr.siUP FAMNIT & IMFM
AfafSaaidiafaf.saaidi (at) gmail.comCNRS/Ecole Polytechnique
NancyRetzlaffnancy (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
ClaraMüllerclara.mueller (at) pharmazie.uni-marburg.deUni Marburg
LudwigBehmTBI_Bled (at) vilera.deUni Marburg
SebastianKrautwurstsebastian.krautwurst (at) uni-jena.deFSU Jena
MichaelRademichael.rade (at) izi.fraunhofer.deFraunhofer IZI
RolfBackofenbackofen (at) informatik.uni-freiburg.deUni Freiburg
SarahBerkemerbsarah (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
MarcusLechnerlechner (at) staff.uni-marburg.deUni Marburg
NikolaiNøjgaardnnoej10 (at) gmail.comSDU Odense
GiuliaCorsigiulia (at) rth.dkRTH Copenhagen
AnneWenzelwenzel (at) rth.dkRTH Copenhagen
AdrianGeissleradrian (at) rth.dkRTH Copenhagen
SvenDziadekdziadek (at) informatik.uni-leipzig.deUni Leipzig, Automaten und Sprachen
TomažPisanskiTomaz.Pisanski (at) upr.siUniversity of Primorska and IMFM
FabianGärtnerFabian (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
ChristianHoener zu Siederdissenchoener (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
AnelaTosevskaatosevska (at) ucla.eduUniversity of California Los Angeles
StefanBadeltbadelt (at) caltech.eduCalifornia Institute of Technology
GregorEntzianentzian (at) tbi.univie.ac.atTBI Wien
Waldeyr MendesSilvamendes (at) iscb.orgUniversity of Brasília
Ana Clara KochMendesmendes (at) iscb.orgUniversity of Brasília
SuemilieKochsuemiliekoch (at) gmail.comuniversity of Brasília
Maria BeatrizWalter Costabia (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
StephanBernhartberni (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
NicolasWiesekewieseke (at) informatik.uni-leipzig.dePaCoSy Leipzig
RomanOchsenreiterromanoch (at) tbi.univie.ac.atTBI Wien
VeerendraGadekarveerendra (at) tbi.univie.ac.atTBI Wien
PatrickBrauna0471164 (at) unet.univie.ac.atTBI Wien
ChristianAnthonanthon (at) rth.dkRTH Copenhagen
JoergFallmannfall (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
KonstantinRiegekonstantin.riege (at) leibniz-fli.deFLI Jena
Jakob HullHavgaardhull (at) rth.dkRTH Copenhagen
Bernhard Thielthiel (at) tbi.univie.ac.atTBI Wien
EmilyThielthiel (at) tbi.univie.ac.atTBI Wien
DominikOttodominik.otto (at) gmail.comFraunhofer IZI
MiladMiladimiladim (at) cs.uni-freiburg.deUni Freiburg
OanaPalascaoana.palasca (at) sund.ku.dkRTH Copenhagen
FlorianHeylheylf (at) informatik.uni-freiburg.deUni Freiburg
AndreFujitaandrefujita (at) gmail.comUniversity of São Paulo
AsukaNakataa.nakata.bs (at) gmail.comKanazawa University
IreneBeckmannirene (at) tbi.univie.ac.atTBI Wien
SwetaSahayswetastar20 (at) gmail.comTBI Wien
BereniceBatutberenice.batut (at) gmail.comUni Freiburg
MariamFarmanfarman (at) tbi.univie.ac.atTBI Wien
MichaSammethmicha (at) sammeth.netBITFUN Lab, Institute of Biophysics (IBCCF), Federal University of Rio de Janeiro (UFRJ)
ManjaMarzmanja (at) uni-jena.deFSU Jena
EliasStadlerstadler (at) bioinf.uni-leipzig.deextern
RolfFagerbergrolf (at) imada.sdu.dkSDU Odense